Metroid: Return to the past
by Phazon-Darren
Summary: After two and half years on the run from the Federation, after the events of Metroid Fusion, Samus is captured by them, demanding she tell them what she knows. She refuses to speak, and with no way of escape, she has to rely on a complete stranger's help!
1. Chapter 1

Metroid: Return To The Past

Chapter 1: The Story Continues

Disclaimer: I do not own Nintendo, Samus or any of its characters mentioned in this fanfic other than O'Connor, which was my own idea. Thanks to NOD-Flareon and Hydros for the help in this chapter.

_**The following take place after the events of Metroid Fusion:**_

The year is 20X8 in the history of the cosmos. Samus Aran (now in her early 30's) was still on the run from the galactic federation, two and a half years on after her near death experience on the B.S.L research station orbiting Planet SR-388, in which she destroyed the X parasites and the entire station.

My name is Samus Aran; I am a freelance bounty hunter. I picked up a distress signal, coming from the area of where the Ceres Space Colony used to be. I decided to investigate, regardless of knowing the Colony no longer existed, thanks to Ridley all those years ago. I arrived at the asteroid field to find nothing but floating debree, probably the remains of the station no doubt. I decided to scan the area just in case, but I found nothing. Suddenly out of nowhere, G-fed ships surround me from all directions!

A trap! How could I have been so stupid?

I was outnumbered by the amount of G-Fed ships, it would be unwise to try and escape, they had obviously planned this carefully. Suddenly a message came up on my screen saying that I should disable my weapons and come peacefully. I decided that it would be wise to follow their instructions, as the odds were not in my favour. Reluctantly, I shut down my weapons and allowed them to transport my ship onto the G-Fed mother ship.

I was removed from my ship and was stripped of my suit and weapons almost immediately. I was then taken to the main interrogation centre aboard the G-Fed Mother Ship. I was questioned to what I had seen back on the B.S.L research station, and the Metroid Production and Research Lab. They wanted to know how much information I had managed to gather up before the section of the station was ejected. I refused to comply with their requests, which probably wasn't the best thing to do, given the situation I was in. Hours passed and still I refused to speak. They put me in a holding cell for what seemed like days.

In that time, I thought about all those years I had worked for the Galactic Federation, destroying potentially deadly creatures and completing near impossible missions that no other dare take on, in return for a sizeable bounty. However, I never joined their organisation. I work alone and that's how it would stay, I do not like taking orders from anyone! All these thoughts went through my mind through the passing days.

Then one day, a tall man with light clothing entered my holding cell. I assumed he must have been some sort of scientist trying to get information out of me, just like the others did. These people will try anything!

"Hello Samus, my name is O'Connor "I thought you would have got the message by now; I am not speaking" I told him. "I don't care if you do, I am here to help you Samus," He said. "Help me? Don't make me laugh! You've done nothing but chase me for the last two and half years, you've done the very opposite of help me!" I shouted at him. "Yes but unfortunately you saw too much back on B.S.L, and the federation had to stop you from ruining their plans" He explained. "Why did you do it? Why would you even think of bringing those things back again after you know what they are capable of!" I Exclaimed. "I agree just as much with you about the whole situation!" he protested. "You…you do?" I said, almost in disbelief.

He sat down on what had been my bed for the last few days.

"Yes Samus, I have tried for a long time to stop this monstrosity from occurring. I voted against their decisions to breed Metroid at B.S.L, but unfortunately I was outvoted and out numbered by my own team. They were like family to me! I took my matter to the head of the Galactic Federation; the council there was already in agreement that the project should go ahead." He explained. "Wasn't there anything that you could have done to prevent this?" I said. "I tried again, but the Federation had stuck by their decision, and I was warned that if I did not let this matter drop, I would be kicked out of the federation for good! There was nothing I could do to stop them. One voice is just not enough to make a difference!" he sighed.

"So why are you telling me this? How do I know your not just saying this to get information out of me?" I said, sitting down beside him.

"Samus, I need your help…I need to stop the federation before it's too late!" He said almost pleading with me. "But I destroyed the station and the Metroids" I exclaimed. "No you didn't Samus, B.S.L was just one of several stations around the galaxy that breaded Metroids, you didn't think the Federation would just have them all in one place did you? Please Samus… we don't have much time! Will you help me stop this project Samus?" He said. "How do I even know your telling me the truth?" I asked him. O'Connor placed his hand inside of his jacket and pulled out an emergency pistol and a key card. "The key card will open the Armament Storage centre on floor 12 area D, in which you will find your suit. When you get it, make your way back to the docking bay, where I shall be waiting for you, and this is how you can trust me" he said, as he handed me the pistol and key card. "And what do you get out of this?" I asked. "I owe it to Adam" said O'Connor. This statement shocked me, as he could probably tell by the expression on my face. "I'll explain later, hurry we don't have a lot of time!" Said O'Connor, and with that, he opened the security doors and walked out of them.

I followed him out of the holding cell, and walked in the opposite direction. How was this O'Connor related to Adam Malkovich? Apart from stopping the Galactic Federation from breeding Metroid, what was in this for him? How would he benefit from this? There's just no way I can possibly trust him

…But what choice did I have?

This is my first ever fanfic, so please read and review, any helpful comments would be much apreciated!


	2. Chapter 2

Metroid: Return To The Past

Chapter 2: In search of the suit

Disclaimer: I do not own Nintendo, Samus or any of its characters mentioned in this fanfic other than O'Connor, which was my own idea. Thanks to NOD-Flareon, Charles and Wayne for their help in this chapter.

I knew I didn't have much time to waste; surely it wouldn't be too long before they discovered I was missing. I made my way down the main corridor; I saw a sign on the wall that confirmed that I was currently on floor 2 section A. I made my way towards the elevator when suddenly; two G-Fed security troopers came out of the elevator and spotted me. "Its Samus!" one of them shouted and they both aimed their weapons at me. I had no choice but to use the Emergency Pistol that O'Connor gave me and I took them both out with 2 single shots.

Just so you know, the Emergency Pistol doesn't kill; it merely paralyses the foe for a short time. I have only used this pathetic excuse of a weapon once before, in desperate times, but I had no time to think about that now, I had to move on.

I made my way towards the elevator and went inside. I pressed down on the elevator and the doors closed behind me. The elevator started to move and I was heading down towards floor 12. This is too easy…

I was correct, a few moments later, there was a sudden halt to the elevator and I was trapped between floors nine and ten. Surely this must have been the work of the G-Fed, they must have found out that I had escaped. My suspicions were confirmed when I heard voices coming from outside the elevator door, then the sounds of metal making contact with metal, they were trying to open the elevator doors, I had been found!

I looked around for a means of escape and noticed a hatch at the top of the elevator. It was my only chance!

I smashed the grating off the hatch and jumped up through it. I got to the top and replaced the hatch where it was, and held myself against the walls of the elevator shaft. Suddenly the doors opened, and I heard voices from below me.

"She must have decided to take the stairs, she tricked us!" said one of the G-Fed troopers. "Well, she can't have gone far, alert troopers throughout the ship to keep a look out, and get a team over to the docking bay to secure her ship, do NOT let her escape!" said another. The troopers' left and when I was sure they had gone, I scrambled back down into the elevator and pushed the down button, to my surprise, the elevator started to move again!

The doors opened and I entered floor 12, I was currently in section A, I had to get to section D as quickly and as stealthily as possible. I came across a few more security troopers along the way, making good use of my Emergency pistol. I finally made it to section D, and walked towards a room with a sign outside of it that said 'Armament Storage' and a slot just below it. I took the card key that O'Connor gave me and placed it in the slot. The doors opened and I stepped inside.

This place was huge! It had almost every type of weapon I had seen the federation use over the years I had worked with them. I didn't have to search for long before I found my suit. I put it on, and did a system scan to find that everything was in working order. I started to walk out of the room when suddenly, the lights in the room glow red and an alarm starts to sound! I ran out of the room only to find myself standing in front of two armed G-Fed Troopers. They started to fire and they gave my suit quite a bit of damage. I had no choice but to defend myself. I charged my power beam and aimed towards the two G-Fed troopers, I unleashed a powerful charge beam attack on them and they were thrown backwards against a wall. I made my way towards the elevator.

I turned the corner only to find a unit of G-Fed Troopers standing there before me. "THERE SHE IS! GET HER!" Shouted the head Trooper. I turned back and started to run. I was chased down a corridor and fired at repeatedly. I came to the end of the corridor and turned right towards the stairs. I started to run up the stairs as fast as I could, from floor to floor while I was been followed from behind.

I got to the top of the stairs and rolled into my morph ball. I bombed the stairs, causing them to collapse behind me, blocking off the G-Fed. I got out of morph ball mode and ran down a corridor towards the docking bay. I turned a few more corners and found the entrance to the docking bay. I shot the security lock off the door and it opened to reveal my ship in the docking bay. "Oh! Samus, you're here!" Shouted a voice from behind the ship. It was O'Connor.

I looked around and saw the bodies of G-Fed troopers scattered everywhere. "What happened here?" I said as I looked around at the sheer destruction. "I had no choice, they was trying to destroy the ship" explained O'Connor. Just then an army of G-Fed troopers began to run into the docking bay. "Quick lets go!" I shouted, and we both scrambled into the ship.

"Start the engines!" commanded O'Connor. "Hey! Nobody tells me what to do, you don't command me!" I said angrily. "Lady, there is an obstruction ahead, I cannot fly us out of here" Said the ship's computer. "Hey that sounds like…" Said O'Connor as the ship, shaken by gunfire from outside, interrupted him. I sat down and took the controls. I fired two missiles at the bay doors and they broke up. I flew my ship out of the G-Fed mother ship and zoomed off into space.

"Adam Malkovich?" O'Connor said in disbelief, looking at the ship's computer screen. "Not exactly, its Adam's digitized mind, programmed into my ship's computer before he died" I said. "I see" Said O'Connor inspecting the computer. "Lady, we are being followed by a fleet of G-Fed ships, would you like me to take action against them?" asked the computer. "Negative, I think we have upset the Federation enough already, lets not take any chances Adam" I told the computer. I looked at my ship's navigation screen to find where we should head to lose the fleet of federation ships chasing us, when I noticed something on the screen that puzzled me.

"Is everything alright?" asked O'Connor. "That's unusual, there's a small rift of some kind on screen, it came up all of a sudden, and I am sure it wasn't there before" I said. "Maybe we could hide there until the Federation pass," said O'Connor. I agreed with O'Connor and set a course for the rift, with the Federation in hot pursuit unsure of what I would find there.

Eventually, we reached the rift, with the Federation still on our tail. According to my scans, the rift hadn't been here long, and I had no clue as to how it was created, but it surely can't have been a natural occurrence. "Lady, the Federation are not far away from us, may I suggest you make a decision now?" asked the computer. "Perhaps if we get close enough to it, we won't show up on scans," said O'Connor. "Take us in closer Adam" I asked the computer. The ship moved in behind the rift and we hid there until the federation passed. They had lost us, and I thought our plan had worked until…

"Lady the rift is expanding, and we are been dragged inside of it!" Said my ship's computer. "Full reverse!" I shouted. Suddenly the ship began to shake and lights began to flicker. "Negative lady, I cannot break free," said the computer. "Do something!" Shouted O'Connor. "DON'T TELL ME WHAT TO DO!" I screamed at O'Connor. The ship began to shake violently and we were drawn into the rift. Suddenly my ship lost power apart from the computer. "Switch to emergency power Adam!" commanded Samus. "Negative Lady, emergency generators are down," announced the computer. "That's it, we are done for!" Shouted O'Connor. "EMERGENCY! EMERGENCY!" said the computer, with power down and with no means of escape; there was nothing I could do.

I enjoyed writing this chapter, it took me a while but I got it done! Please read and review, and I hope to bring you the third chapter really soon!


	3. Chapter 3

Metroid: Return To The Past 

**Chapter 3: A Journey through time**

"We survived! I can't believe we survived!" were the first words I heard coming from O'Connor as I awoke with a terrible headache.

"Good to have you back lady," said the unmistakeable voice of Adam, my ship's computer. I took off my helmet and held my head. "What…what happened?" I asked, trying to make sense of the situation. "Take it easy Samus, you had a nasty fall. You were knocked out cold!" explained O'Connor. "What's the state of the ship?" I asked, sitting up. "Bad news I'm afraid Samus. The ship has taken quite a bit of damage, and so have you. All of your weapons and abilities are offline, I am surprised we came out of the rift in one piece!" said a relieved O'Connor.

I climbed up onto my seat and tapped the computer's navigation screen, turning it on. "I hate to ask silly questions, but where the hell did we come out to?" I asked. "Good question lady, we appear to be in orbit above planet Tallon III. We are not too far away from Planet Zebes, except…" the computer said, trailing off. "Except what Adam?" I asked, worried. "…We aren't even in the same time and space lady," said the computer. I found this hard to believe at first, but after scanning the area, I realised that the computer was correct!

"It seems that we entered some sort of tear in time and space itself" explained O'Connor. "How far back have we actually gone?" I asked. "We haven't been able to determine how far back exactly, but we think around fifteen years or so," explained O'Connor.

Fifteen years ago? That was before I even set out on my first ever mission, against the space pirates. I was still training to be what I am today.

"What if we were to fly back through it again?" I asked. "Negative lady, shields are down. We are just scraping along on emergency power," explained the computer. "We have to do something!" I exclaimed. "I think it would be wise to land the ship on Tallon III and carry out repairs on the ship," said O'Connor calmly, placing his hand on my shoulder.

I nodded and took to the controls of my ship. I set the co-ordinates for an abandoned research site on Tallon III's surface. My ship began to enter Tallon III's atmosphere and began its decent towards the planets surface.

**TALLON III**

**Mass: 4.7 Trillion Teratons**

**Profile: Smaller in mass than Planet Zebes, it has an atmosphere almost the same as Tallon IV, its sister planet. Once populated by the Chozo, this planet was a thriving planet, a tropical paradise. **

**Scans show Phazon Radiation has infected the planet and is slowly destroying life there, similar to Tallon IV, but at a much faster rate. Scans show minimal life signs on the plant's surface. **

**Intelligent life not detected.**

My ship descended through the atmosphere and landed on the ground without any trouble. I scanned the area one final time to make sure there were no life signs, and when I was certain there was nothing around, I put my helmet on and prepared to leave the ship. "Samus, all your weapons are offline except your power beam and your scan visor," said O'Connor. "I'll be fine" I told him, and walked out of the ship.

As I stepped foot into the open, I saw a beautiful area, full of forests, waterfalls and a lake. Beyond it in the distance, were some ruins, and the research site. I made my way towards the ruins. Along the way, I crossed a narrow bridge, close to a waterfall. As I progressed towards the ruins, I had a strange feeling I was been watched… followed even. I turned around, and used my scan visor to scan the area around me. There was nothing to be seen.

When I finally reached the ruins, I discovered that it was a large Chozo temple. I aimed my arm cannon towards the temple door and fired a single shot of energy towards it, and it opened without any trouble. I slowly stepped inside, not knowing what sort of things I would find there.

Inside the temple, I saw computers and control panels everywhere! There were containers too, that probably once used to hold animal specimens. It became clear to me that this research base had not been used in such a long time, and there would be little chance of me finding any sort of materials to repair my ship. I decided to do a scan of the research room in hope that I would find something useful.

I scanned the containers to see what was inside them. My scans detected nothing at first, but suddenly, it picked up on something inside one of the containers! It was some sort of machine, but my scan couldn't pick up exactly what it was. I went over to the container, and with a couple of shots at the lock of the container, it opened. Inside was a Chozo built Arm Cannon upgrade, which seemed to be in perfect working order, and just so happened to be compatible with my suit!

Charge Beam Acquired!

I started to make my way out of the temple, when suddenly, the door of the temple sealed, and I was trapped! I then heard a voice from behind me…

"Samus Aran! I have been expecting you!" said the voice.

I charged my power beam and aimed towards the voice, and noticed a figure of some kind was standing directly opposite me, obscured by shadow. Was this person a friend or a foe? I was about to find out, as the figure started walking slowly out of the darkness towards me.

Another cliffhanger! Sorry about that everyone. Please read and review and let me know what you thought of this chapter!


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